Clover is a program for identifying functional sites in DNA sequences. If you give it a set of DNA sequences that share a common function, it will compare them to a library of sequence motifs (e.g. transcription factor binding patterns), and identify which, if any, of the motifs are statistically overrepresented in the sequence set. (source: http://cagt.bu.edu/page/Clover_about)
In some instances, it may be desirable to query the text output of Clover to identify a set of genes that share a common transcription factor binding site. For instance, if you are interested in FOX3, you may query the Clover output for FOX3 and get a list of genes that have FOX3 as a statistically overrepresented transcription factor binding pattern.
python3 query.py <clover_file.txt> Enter TF: <TF_name>
The output is a CSV file with a list of all Ensembl IDs of genes that have <TF_name> as a statistically over-represented TF.
The query does not perform a regular expression search. Instead, it looks for the name of the TF exactly as specified by the user. There are transcriptions factors that have variations in their name (e.g. FOXO3A, FOXO3B).